Structure of PDB 7y02 Chain A Binding Site BS02

Receptor Information

>7y02 Chain A (length=263) Species: 3988 (Ricinus communis)

QYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPIN
QRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAI
THLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYY
STGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSV
ITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIAL
MVYRCAPPPSSQF

Ligand information

• Ligand ID: IEZ
• InChI: InChI=1S/C16H13FN6O4/c17-8-3-1-7(2-4-8)5-9(15(26)27)21-13(24)10-6-19-11-12(20-10)22-16(18)23-14(11)25/h1-4,6,9H,5H2,(H,21,24)(H,26,27)(H3,18,20,22,23,25)/t9-/m0/s1
• InChIKey: AGGHEPSDSCKUEM-VIFPVBQESA-N
• SMILES:
  CACTVS 3.385: NC1=Nc2nc(cnc2C(=O)N1)C(=O)N[C@@H](Cc3ccc(F)cc3)C(O)=O
  OpenEye OEToolkits 2.0.7: c1cc(ccc1C[C@@H](C(=O)O)NC(=O)c2cnc3c(n2)N=C(NC3=O)N)F
  OpenEye OEToolkits 2.0.7: c1cc(ccc1CC(C(=O)O)NC(=O)c2cnc3c(n2)N=C(NC3=O)N)F
  CACTVS 3.385: NC1=Nc2nc(cnc2C(=O)N1)C(=O)N[CH](Cc3ccc(F)cc3)C(O)=O
• Formula: C16 H13 F N6 O4
• Name: (2S)-2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]-3-(4-fluorophenyl)propanoic acid;
  (S)-2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)-3-(4-fluorophenyl)propanoic acid
• PDB chain: 7y02 Chain A Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7y02 Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): D75 N78 Y80 D96 D100 W211 R258
• Binding residue (residue number reindexed from 1): D71 N74 Y76 D92 D96 W207 R254
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.2.2.22: rRNA N-glycosylase.

Gene Ontology

Molecular Function

• GO:0030598 rRNA N-glycosylase activity

Biological Process

• GO:0017148 negative regulation of translation

External links

• PDB: RCSB:7y02, PDBe:7y02, PDBj:7y02
• PDBsum: 7y02
• PubMed: 35998389
• UniProt: P02879|RICI_RICCO Ricin